A Strategy for Suppressing Redox Stress within Mitochondria

An aza analogue (1) of the experimental neuroprotective drug idebenone has been prepared and evaluated. The compound quenches lipid peroxidation more effectively than α-tocopherol and potently suppresses reactive oxygen species in cells under oxidative stress. It is thought to do so via a catalytic cycle in which both forms of oxidative stress are suppressed simultaneously. Consequently, the compound effectively protects cultured CEM leukemia cells and Friedreich's ataxia fibroblasts from oxidative stress more effectively than idebenone or idebenol.

Structural basis for the exceptional stability of bisaminoacylated nucleotides and transfer RNAs

At least one bisaminoacyl-tRNA is synthesized in nature (by Thermus thermophilus phenylalanyl-tRNA synthetase), and many disubstituted tRNAs have been prepared in vitro. Such misacylated tRNAs are able to participate in protein synthesis, even though they lack the free 2'-OH group of the 3'-terminal adenosine moiety. Their ready participation in protein synthesis implies significant chemical reactivity. The basis for this reactivity has been documented previously. Surprisingly, the aminoacyl moieties of these tRNAs also exhibit exceptional chemical stability. In the present report, bisaminoacylated nucleotides are investigated computationally and experimentally to define the basis for the stability of such species. Molecular modeling of bisalanyl-AMP in the absence of solvent and in the presence of a limited number of water molecules revealed two common features among the low-energy structures. The first was the presence of H-bonding interactions between the two aminoacyl moieties. The second was the presence of a H-bonding interaction between the 2'-O-alanyl moiety and the N-3 atom of the adenine nucleobase, typically mediated through a water molecule. The prediction of an interaction between an aminoacyl moiety and the adenine nucleobase was confirmed experimentally by comparing the behavior of bisalanyl-AMP and bisalanyl-UMP in the presence of model nucleophiles. This study suggests a possible role for the adenosine moiety at the 3'-end of aminoanyl-tRNAs in controlling the stability and reactivity of the aminoacyl moiety and has important implications for the reactivity and stability of normal aminoacyl-tRNAs.

Synthesis and characterization of mitoQ and idebenone analogues as mediators of oxygen consumption in mitochondria

Analogues of mitoQ and idebenone were synthesized to define the structural elements that support oxygen consumption in the mitochondrial respiratory chain. Eight analogues were prepared and fully characterized, then evaluated for their ability to support oxygen consumption in the mitochondrial respiratory chain. While oxygen consumption was strongly inhibited by mitoQ analogues 2-4 in a chain length-dependent manner, modification of idebenone by replacement of the quinone methoxy groups by methyl groups (analogues 6-8) reduced, but did not eliminate, oxygen consumption. Idebenone analogues 6-8 also displayed significant cytoprotective properties toward cultured mammalian cells in which glutathione had been depleted by treatment with diethyl maleate.

Does oxidative stress contribute to the pathology of Friedreich's ataxia? A radical question

Friedreich's ataxia (FRDA) is a hereditary neurodegenerative disease that frequently culminates in cardiac failure at an early age. FRDA is believed to arise from reduced synthesis of the mitochondrial iron chaperone frataxin due to impaired gene transcription, which leads to mitochondrial iron accumulation, dysfunction of mitochondrial Fe-S containing enzymes, and increased Fenton-mediated free radical production. Recent reports have challenged this generally accepted hypothesis, by suggesting that the oxidative stress component in FRDA is minimal and thereby questioning the benefit of antioxidant therapeutic strategies. We suggest that this apparent paradox results from the radically divergent chemistries of the participating reactive oxygen species (ROS), the major cellular subcompartments involved and the overall cellular responses to ROS. In this review, we consider these factors and conclude that oxidative stress does constitute a major contributing factor to FRDA pathology. This reaffirms the idea that the rational design of specific small molecule multifunctional antioxidants will benefit FRDA patients.

Cytokinins: synthesis, mass spectra, and biological activity of compounds related to zeatin

Compounds related to dihydrozeatin that define the influence of the location of the hydroxyl group along the side chain have been synthesized and tested for cytokinin activity. The compounds compared are in the series: 6-(X-hydroxy-3-methylbutylamino)purines and their ribosides, where X = 2, 3, and 4.Hydroxy substitution on the 4-position of the side chain enhances, but in the 2-, 3-, or 2- and 3- positions, decreases cytokinin activity as compared with the unsubstituted isopentyl (or isopentenyl) chains. This differential influence of the position of the hydroxyl group in the N(6)-chain holds also for the similarly related 9-beta-D-ribofuranosides. The relatively higher activity of 3,4-dihydroxy as compared with 2,3-dihydroxy derivatives is consistent with this position effect.Compounds related to zeatin possessing side-chain ester moieties have also been synthesized and tested comparatively. Among these, 6-(4-acetoxy-3-methyl-trans-2-butenylamino)purine is at least as active as zeatin, the most active presently known cytokinin in the tobacco bioassay, whereas the analog, methyl 2-methyl-4-(purin-6-ylamino)-trans-crotonate, with the ester function effectively reversed, has vastly lower activity, and its riboside is practically inactive.

Anticytokinin activity of substituted pyrrolo[2,3-d]pyrimidines

Ten substituted pyrrolo[2,3-d]pyrimidines were tested as cytokinins and anticytokinins in the tobacco bioassay. Eight new anticytokinins were identified and two were found to be highly active. The most potent species were 4-cyclohexylamino- and 4-cyclopentylamino-2-methylthiopyrrolo[2,3-d]pyrimidine, of which 0.05 and 0.009 muM concentrations, respectively, were required to produce detectable inhibition of the growth of tobacco callus cultured on a medium containing 0.003 muM 6-(3-methyl-2-butenylamino)purine. The inhibition of growth by moderate (</=6.6 muM) concentrations of these compounds was reversible by equal or higher concentrations of 6-(3-methyl-2-butenylamino)purine, but not by indole-3-acetic acid or gibberellic acid. These substituted pyrrolo[2,3-d]pyrimidines were also found to enhance bud formation at high cytokinin concentrations, suggesting that a cytokinin may act at more than one cellular site in exerting its growth-promoting and morphogenetic effects.

Synthesis and evaluation of verticipyrone analogues as mitochondrial complex I inhibitors

Verticipyrone has recently been isolated from the culture broth of Verticillium sp. and shown to inhibit NADH fumarate reductase, as well as NADH oxidoreductase (complex I) of the mitochondrial electron transport chain. In order to assess the structural elements in verticipyrone essential for complex I inhibitor, 15 structural analogues were prepared and analyzed for their effects on mitochondrial NADH oxidoreductase and NADH oxidase activities. Also measured were the abilities of several of the analogues to inhibit respiration as judged by a shift to glycolysis, and to inhibit the growth of several mammalian cell lines. The nature of the pyrone ring was shown to be important to potency of inhibition, as was the length and nature of substituents in the side chain of the analogues.

The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern

Transcriptional regulation of the bcl-2 proto-oncogene is highly complex, with the majority of transcription driven by the P1 promoter site and the interaction of multiple regulatory proteins. A guanine- and cytosine-rich (GC-rich) region directly upstream of the P1 site has been shown to be integral to bcl-2 promoter activity, as deletion or mutation of this region significantly increases transcription. This GC-rich element consists of six contiguous runs of guanines and cytosines that have the potential to adopt DNA secondary structures, the G-quadruplex and i-motif, respectively. Our laboratory has previously demonstrated that the polypurine-rich strand of the bcl-2 promoter can form a mixture of three different G-quadruplex structures. In this current study, we demonstrate that the complementary polypyrimidine-rich strand is capable of forming one major intramolecular i-motif DNA secondary structure with a transition pH of 6.6. Characterization of the i-motif folding pattern using mutational studies coupled with circular dichroic spectra and thermal stability analyses revealed an 8:5:7 loop conformation as the predominant structure at pH 6.1. The folding pattern was further supported by chemical footprinting with bromine. In addition, a novel assay involving the sequential incorporation of a fluorescent thymine analog at each thymine position provided evidence of a capping structure within the top loop region of the i-motif. The potential of the GC-rich element within the bcl-2 promoter region to form DNA secondary structures suggests that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 transcriptional regulation. Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition.

Calothrixins, a new class of human DNA topoisomerase I poisons

Calothrixins A (1) and B (2) were converted to their O- and N-methylated derivatives, respectively. All four compounds were found to act as poisons of DNA topoisomerase I and to do so reversibly. Three of the calothrixins (1-3) were tested for their cytotoxicity toward cultured (p53 proficient) CEM leukemia cells and found to exhibit IC(50) values ranging from 0.20 to 5.13 muM. The cell cycle effects of calothrixins 1-3 were also studied. Calothrixin B (2) produced G(1) arrest at 0.1 muM concentration, while higher concentrations of calothrixins 1 and 3 resulted in cell accumulation in both the S and G(2)/M phases of the cell cycle. The cell cycle effects produced by the calothrixins were more readily reversible upon removal of the compounds than those produced by camptothecin.

Carbohydrate dependent targeting of cancer cells by bleomycin-microbubble conjugates

Biotinylated bleomycin A(5) was attached to streptavidin-derivatized microbubbles, and a solution containing the conjugate was passed over a monolayer of cultured MCF-7 cells. The bleomycin-derivatized microbubbles adhered to the MCF-7 cells, and the association could be monitored by the use of a microscope. Three other cancer cell lines gave similar results. The bleomycin-microbubble conjugate did not bind to a normal breast cell line (MCF-10A) or to the matched noncancer cell lines corresponding to the other cancer cell lines targeted by bleomycin. No binding to any tested cell line was observed when the microbubbles lacked conjugated bleomycin A(5) or when the microbubble contained a bleomycin A(5) analogue lacking the carbohydrate moiety.

Identification of strong DNA binding motifs for bleomycin

The bleomycins (BLMs) are clinically used antitumor antibiotics. Their mechanism of action is believed to involve oxidative cleavage of DNA and possibly also RNA degradation. DNA degradation has been studied extensively and shown to involve binding of an activated metallobleomycin to DNA, followed by abstraction of C4'-H from deoxyribose in the rate-limiting step for DNA degradation. It is interesting that while DNA and RNA degradation by activated Fe.BLM has been studied extensively, much less is known about the actual binding selectivity of BLM, that is, the obligatory step that precedes cleavage. Thus it is unclear whether cleavage specificity is defined by the binding event or whether cleavage occurs at a subset of preferred binding sites. With only a few exceptions, NMR binding studies have employed metalloBLMs such as Co.BLM and Zn.BLM whose therapeutic relevance is uncertain. A single biochemical study that compared DNA binding and cleavage directly also employed Co.BLM. It is logical to anticipate that preferred sites of DNA cleavage will occur at sites that are (a subset of) preferred DNA binding sites, but there are currently no data available relevant to this issue. Herein, we describe the development and implementation of a novel strategy to identify DNA motifs that bind BLM strongly.

Aminoacylation of transfer RNAs with one and two amino acids

The detailed synthesis of (bis)aminoacyl-pdCpAs and the corresponding singly and tandemly activated tRNAs is reported. The synthetic pathway leading to these compounds has been validated for simple amino acid residues as well as for amino acids bearing more complex side chains. Protection/deprotection strategies are described. For the bisaminoacylated tRNAs, both the synthesis of tRNAs bearing the same amino acid residue at the 2' and 3' positions and tRNAs bearing two different aminoacyl moieties are reported. Further, it is shown that the tandemly activated tRNAs are able to participate in protein synthesis.

Chemical and traditional mutagenesis of vaccinia DNA topoisomerase provides insights to cleavage site recognition and transesterification chemistry

Vaccinia DNA topoisomerase IB (TopIB) relaxes supercoils by forming and resealing a covalent DNA-(3'-phosphotyrosyl)-enzyme intermediate. Here we gained new insights to the TopIB mechanism through "chemical mutagenesis." Meta-substituted analogs of Tyr(274) were introduced by in vitro translation in the presence of a chemically misacylated tRNA. We report that a meta-OH reduced the rate of DNA cleavage 130-fold without affecting the rate of religation. By contrast, meta-OCH(3) and NO(2) groups elicited only a 6-fold decrement in cleavage rate. We propose that the meta-OH uniquely suppresses deprotonation of the para-OH nucleophile during the cleavage step. Assembly of the vaccinia TopIB active site is triggered by protein contacts with a specific DNA sequence 5'-C(+5)C(+4)C(+3)T(+2)T(+1)p downward arrowN (where downward arrow denotes the cleavage site). A signature alpha-helix of the poxvirus TopIB ((132)GKMKYLKENETVG(144)) engages the target site in the major groove and thereby recruits catalytic residue Arg(130) to the active site. The effects of 11 missense mutations at Tyr(136) highlight the importance of van der Waals interactions with the 3'-G(+4)pG(+3)p dinucleotide of the nonscissile strand for DNA cleavage and supercoil relaxation. Asn(140) and Thr(142) donate hydrogen bonds to the pro-(S(p))-oxygen of the G(+3)pA(+2) phosphodiester of the nonscissile strand. Lys(133) and Lys(135) interact with purine nucleobases in the major groove. Whereas none of these side chains is essential per se, an N140A/T142A double mutation reduces the rate of supercoil relaxation and DNA cleavage by 120- and 30-fold, respectively, and a K133A/K135A double mutation slows relaxation and cleavage by 120- and 35-fold, respectively. These results underscore functional redundancy at the TopIB-DNA interface.

Inhibitors of DNA polymerase beta: activity and mechanism

Bioassay-guided fractionation of extracts prepared from Couepia polyandra and Edgeworthia gardneri resulted in the isolation of the DNA polymerase beta (pol beta) inhibitors oleanolic acid (1), edgeworin (2), betulinic acid (3), and stigmasterol (4). Study of these pol beta inhibitors revealed that three of them inhibited both the lyase and polymerase activities of DNA polymerase beta, while stigmasterol inhibited only the lyase activity. Further investigation indicated that the four inhibitors had substantially different effects on the DNA-pol beta binary complex that is believed to be an obligatory intermediate in the lyase reaction. It was found that the inhibitors potentiated the inhibitory action of the anticancer drug bleomycin in cultured A549 cells, without any influence on the expression of pol beta in the cells. The results of the unscheduled DNA synthesis assay support the thesis that the potentiation of bleomycin cytotoxicity by DNA pol beta inhibitors was a result of an inhibition of DNA repair synthesis.